6810: 1094 Activities 1

Please work in pairs with comparable computing and physics experience.
The instructors will bounce around 1094 and answer questions
(ask about anything!).
Fill out and hand in this sheet at the end of class.

GNU-Unix Environment with Cygwin (If you want to use Windows)

"Switch user" from Shut down menu and log on to your Physics Department
Windows account (username should be your name.#).

We recommend that you use the shared disk set up for Physics 6810.
To do so, click on the Start menu and right-click on Computer.
Select "Map Network Drive" and type \\phypcs\physics 780
for the Folder. Select a drive letter (Z: is a good choice).
Now you can create a working directory ("folder") on this drive with
a unique name (e.g., your name).

Start up a web browser. Go to the 6810 home page
(http://www.physics.ohio-state.edu/~ntg/6810/) and find the
session01.zip file (under Codes) and unzip it
into your 6810 folder (choose "Open with Windows Explorer" and
then select it and "Extract all files" is one way to do this).
You will also be able to unzip it from the Cygwin command line if you
save it to your 6810 folder.

Go to "All programs" under the Start menu and find Cygwin-X. You will
find (too) many choices; for now, choose LXDE. This starts up a "window
manager", from which you can pop up terminal windows and other
programs using the menus at the
lower left. The main menu is all the way to the left with the LXDE logo
(it's supposed to be a bird :).
Start at least one terminal (from the terminal icon is easiest; I like System Tools -> Terminal
better).

Take a look at the unix command summary handout.
Type pwd ("present working directory") to see where
you are. Change to the 6810 directory with (if your working folder
is on the Z drive)
cd /cygdrive/z
and then use cd to go to your working directory
you created above and then the session_01 subdirectory.
Use the tab
key for "name completion" (try it!).

GNU-Unix Environment (If you want to use Linux)

If your computer is in Windows, logoff and "restart".
Just after the Dell screen, there will be a countdown --- hit any key to
stop it.
At the Grub
prompt, use the arrows to highlight "Linux" (Red Hat ...)
and hit return.
Same name.1 username and password as with Windows.

Right click on background for a menu with "Open in Terminal". Start up
one or two terminal windows.

Take a look at the unix command summary sheet.
Create a directory for 6810 ("mkdir 6810"), go to that directory
("cd 6810").

Figure out how to
launch a web browser (look under "Applications"),
find the 6810 homepage
(http://www.physics.ohio-state.edu/~ntg/6810/) and
download session01.zip (from "Codes") into the 6810 directory.
Unpack it with "unzip session01.zip", which should create the
session_01 subdirectory with some files in it.
Go to the session_01 subdirectory.

A Simple C++ Program (look at the file first in an editor!)

Make a note below of anything you don't understand about the code
for the simple program area.cpp.
(If you are new to C++ or just rusty, you might not understand
much; see the discussion in the background notes for some
details.)
Editor: use nedit or emacs or vi or ...
(I suggest using nedit if you don't
know any of these) to look at area.cpp.
E.g., type nedit area.cpp &. (The "&" runs the editor in the
"background" so the terminal is still available.)
Why use "area" and "radius" for variables rather than "A"
and "R", which are quicker to type?

Compile and link area.cpp to create area.x (or area.exe on Windows) using
g++ -o area.x area.cpp
(the executable would be called a.out if you left out "-o area.x").
Run it by typing "area.x" (or "./area.x" if you get an error
message about not finding the file; why does this work?).
Add "<< endl" to the end of the output line (starting "cout ...")
and recompile and rerun.
What did this do?

To get used to error messages, modify the program to create
some errors and see what
the compiler says (try these then invent your own):

remove a semi-colon (leaving out a ; is the most common
error you will make!)

use // to comment out using namespace std;
[fix this by adding std::]

remove a } (or change it from "}" to ")" or "]")

Each time, try compiling again. The compiler should give an error
message with the line number it thinks is a problem and an explanation
(which is often not helpful!). Fix the error and make sure the program
still works. Note that "not declared"
errors are reported as being at different lines than where
the error is made. Why aren't they noticed immediately?

List two ways to verify that the program is
giving correct answers using known special cases and scaling
arguments (e.g., multiply radius by factors of 10):

Later (in PS#1) you will be asked to
carry out some of the "to do" list in the comments (with assistance, as needed).
Which, if any, of them do you know how to do now?

Copy, rename, and modify area.cpp to make a program
volume.cpp, which calculates
the volume of a sphere using V = (4/3)πr3. Test it. [Warning: Many people
get this wrong the first time. Test carefully!]

Let's try Python!
Look at area0.py in the editor,
and run it (python area0.py is one way).
Compare with the C++ version.
Do they have the same pseudocode? List three differences
between the C++ and Python implementations.

Overflows, Underflows, and Machine Precision

Refer to the background notes on number representation as you do this
section.

Look at the file for the code "flows.cpp".
Where does the output go?
A single-precision number in C++ is a "float" and a
double-precision number in C++ is a "double".
You are to empirically determine (in base 10, not powers of 2)
(put your answers in the blank
spaces and compare to the notes)

where underflow and overflow occur for single-precision
floating-point numbers;

where underflow and overflow occur for double-precision
floating-point numbers.

Now for the machine precision, which is calculated crudely in
"precision.cpp".
[Note: This code has an intentional bug. Compare to
flows.cpp to track it down.]
Determine empirically (in base 10)

the machine precision for single-precision
floating-point numbers;

the machine precision for double-precision
floating-point numbers. [Note: you have to change
the code for this to work correctly. Hint:
the correct answer is smaller than 1e-12.]

Explain briefly what
the machine precision is and how
it is found (note the output file):

Using a Makefile

Look at the makefile "make_area" in an editor.
Makefiles are useful tools to organize the code for computational
physics projects.
They contain instructions for how to build an executable (what files
have the code, what options to use in compiling, what libraries to link
to).
Here we have only one source (.cpp) file, but the makefile
keeps track of all the g++ options.

Look at make_area in an editor. We'll go through the details of
a makefile later; for now note the following:

Comments start with "#" and continuation lines
are indicated by "\" (so "SRCS= \" and "area.cpp" is all on one line).
[Warning: There can't be any spaces after the "\".]

The list of options defined by "WARNFLAGS" are options to g++
(see C++ options handout for details).

Run the makefile using "make -f make_area". It will try to
compile area.cpp and then link to create area.x. Did it work?

Make a copy of make_area ("cp make_area make_flows") and
edit it so that it compiles and links flows.cpp.
[Follow the instructions in the makefile.]
Success?

Using the GSL Scientific Library

A link to the full GSL documentation can be
found on the 6810 web page. Here we look at our first
example program, which has been adapted
from the documentation.

Examine the file "J0_test.cpp" in
an editor. This test program calculates the cylindrical Bessel
function J0(x) at x=5 using the GSL library function
"gsl_sf_bessel_J0" (you would find out the name of the function by looking
at the web page with the GSL reference manual).
Look up "Bessel function Wikipedia" using Google. How can
you use a graph on the webpage
to check you are calculating the right thing?

Compile J0_test.cpp according to the directions in the file and
verify that the correct answer is given. Is it?

Now calculate for x=3
(modify the code for this value or add code to read in any x).
Answer:

Verify your answer using Mathematica or MATLAB or Python.
If Mathematica, under the Help menu,
start the Help Browser, choose "Master Index", and look under Bessel
function).
If MATLAB, under the Help menu, select "MATLAB Help", choose
"Search Results", and search for "Bessel Functions".
Did you succeed?

Discuss with your partner how a more general program could
be structured, and make at least two suggestions here.

Some More Python (if time permits)

Create volume0.py.

Look at and run the Python versions of the flows and precision
codes (included in session01.zip).

Try running Python interactively. At the prompt, just
type python and return. You will get a
>>> prompt. Try import area1 and then
help(area1). Use quit() to exit.
(On Linux you will need to type /usr/bin/python.)

Tkinter demo: Look at hello_world_gui.py and run it. Try to
change the text and font.

Sharing Your Session Using BuckeyeBox

We're going to try BuckeyeBox to share
files (also your homework with the instructors!).
***You have to activate this with your name.# account and email
address through
my.osu.edu*** (other email addresses, such as gmail, won't work).

If you haven't activated your BuckeyeBox account,
go to https://box.osu.edu/ and
follow the instructions under "Sign Up".
(You will first login to my.osu.edu and then you will be taken to
a "Manage BuckeyeBox" page, where you can enable it.)

From the box.osu.edu page, "Log In" to see your BuckeyeBox folders.

Click on the "+ New" icon to create a new Folder and name it
"6810_last name_first name" (where you substitute
your own names, e.g., "6810_Furnstahl_Dick").
Invite furnstahl.1@osu.edu and smith.10851@osu.edu "to upload or download
files" (access type: Editor).

Now go into your new folder. Use "Upload" to upload the Session_01
folder.
Did you succeed? (note any problems here)

You can setup BuckeyeBox Sync on your own computer to automagically
synchronize a local version of the file with the one in the cloud!